fractal-server 1.4.10__py3-none-any.whl → 2.0.0a1__py3-none-any.whl

fractal_server/app/schemas/{task.py → v1/task.py}

@@ -6,18 +6,18 @@ from pydantic import Field
 from pydantic import HttpUrl
 from pydantic import validator
 
-from ._validators import valstr
+from .._validators import valstr
 
 __all__ = (
-    "TaskCreate",
-    "TaskUpdate",
-    "TaskRead",
-    "TaskImport",
-    "TaskExport",
+    "TaskCreateV1",
+    "TaskUpdateV1",
+    "TaskReadV1",
+    "TaskImportV1",
+    "TaskExportV1",
 )
 
 
-class _TaskBase(BaseModel):
+class _TaskBaseV1(BaseModel):
     """
 
     Base class for `Task`.
@@ -32,7 +32,7 @@ class _TaskBase(BaseModel):
     _source = validator("source", allow_reuse=True)(valstr("source"))
 
 
-class TaskUpdate(_TaskBase):
+class TaskUpdateV1(_TaskBaseV1):
     """
     Class for `Task` update.
 
@@ -76,7 +76,7 @@ class TaskUpdate(_TaskBase):
     )
 
 
-class TaskImport(_TaskBase):
+class TaskImportV1(_TaskBaseV1):
     """
     Class for `Task` import.
     """
@@ -84,7 +84,7 @@ class TaskImport(_TaskBase):
     pass
 
 
-class TaskExport(_TaskBase):
+class TaskExportV1(_TaskBaseV1):
     """
     Class for `Task` export.
     """
@@ -92,7 +92,7 @@ class TaskExport(_TaskBase):
     pass
 
 
-class TaskRead(_TaskBase):
+class TaskReadV1(_TaskBaseV1):
     """
     Class for `Task` read from database.
 
@@ -124,7 +124,7 @@ class TaskRead(_TaskBase):
     docs_link: Optional[HttpUrl]
 
 
-class TaskCreate(_TaskBase):
+class TaskCreateV1(_TaskBaseV1):
     """
     Class for `Task` creation.
 

fractal_server/app/schemas/{task_collection.py → v1/task_collection.py}

@@ -6,16 +6,16 @@ from pydantic import BaseModel
 from pydantic import Field
 from pydantic import validator
 
-from ._validators import valstr
-from .task import TaskRead
+from .._validators import valstr
+from .task import TaskReadV1
 
 __all__ = (
-    "TaskCollectPip",
-    "TaskCollectStatus",
+    "TaskCollectPipV1",
+    "TaskCollectStatusV1",
 )
 
 
-class TaskCollectPip(BaseModel):
+class TaskCollectPipV1(BaseModel):
     """
     TaskCollectPip class
 
@@ -81,7 +81,7 @@ class TaskCollectPip(BaseModel):
         return v
 
 
-class TaskCollectStatus(BaseModel):
+class TaskCollectStatusV1(BaseModel):
     """
     TaskCollectStatus class
 
@@ -97,7 +97,7 @@ class TaskCollectStatus(BaseModel):
     status: Literal["pending", "installing", "collecting", "fail", "OK"]
     package: str
     venv_path: Path
-    task_list: Optional[list[TaskRead]] = Field(default=[])
+    task_list: Optional[list[TaskReadV1]] = Field(default=[])
     log: Optional[str]
     info: Optional[str]
 

fractal_server/app/schemas/{workflow.py → v1/workflow.py}

@@ -6,30 +6,30 @@ from typing import Optional
 from pydantic import BaseModel
 from pydantic import validator
 
-from ._validators import valint
-from ._validators import valstr
-from ._validators import valutc
-from .project import ProjectRead
-from .task import TaskExport
-from .task import TaskImport
-from .task import TaskRead
+from .._validators import valint
+from .._validators import valstr
+from .._validators import valutc
+from .project import ProjectReadV1
+from .task import TaskExportV1
+from .task import TaskImportV1
+from .task import TaskReadV1
 
 __all__ = (
-    "WorkflowCreate",
-    "WorkflowRead",
-    "WorkflowUpdate",
-    "WorkflowImport",
-    "WorkflowExport",
-    "WorkflowTaskCreate",
-    "WorkflowTaskImport",
-    "WorkflowTaskExport",
-    "WorkflowTaskRead",
-    "WorkflowTaskUpdate",
-    "WorkflowTaskStatusType",
+    "WorkflowCreateV1",
+    "WorkflowReadV1",
+    "WorkflowUpdateV1",
+    "WorkflowImportV1",
+    "WorkflowExportV1",
+    "WorkflowTaskCreateV1",
+    "WorkflowTaskImportV1",
+    "WorkflowTaskExportV1",
+    "WorkflowTaskReadV1",
+    "WorkflowTaskUpdateV1",
+    "WorkflowTaskStatusTypeV1",
 )
 
 
-class _WorkflowTaskBase(BaseModel):
+class _WorkflowTaskBaseV1(BaseModel):
     """
     Base class for `WorkflowTask`.
     """
@@ -38,7 +38,7 @@ class _WorkflowTaskBase(BaseModel):
     args: Optional[dict[str, Any]] = None
 
 
-class WorkflowTaskCreate(_WorkflowTaskBase):
+class WorkflowTaskCreateV1(_WorkflowTaskBaseV1):
     """
     Class for `WorkflowTask` creation.
 
@@ -51,7 +51,7 @@ class WorkflowTaskCreate(_WorkflowTaskBase):
     _order = validator("order", allow_reuse=True)(valint("order", min_val=0))
 
 
-class WorkflowTaskRead(_WorkflowTaskBase):
+class WorkflowTaskReadV1(_WorkflowTaskBaseV1):
     """
     Class for `WorkflowTask` read from database.
 
@@ -67,10 +67,10 @@ class WorkflowTaskRead(_WorkflowTaskBase):
     order: Optional[int]
     workflow_id: int
     task_id: int
-    task: TaskRead
+    task: TaskReadV1
 
 
-class WorkflowTaskImport(_WorkflowTaskBase):
+class WorkflowTaskImportV1(_WorkflowTaskBaseV1):
     """
     Class for `WorkflowTask` import.
 
@@ -78,10 +78,10 @@ class WorkflowTaskImport(_WorkflowTaskBase):
         task:
     """
 
-    task: TaskImport
+    task: TaskImportV1
 
 
-class WorkflowTaskExport(_WorkflowTaskBase):
+class WorkflowTaskExportV1(_WorkflowTaskBaseV1):
     """
     Class for `WorkflowTask` export.
 
@@ -89,10 +89,10 @@ class WorkflowTaskExport(_WorkflowTaskBase):
         task:
     """
 
-    task: TaskExport
+    task: TaskExportV1
 
 
-class WorkflowTaskUpdate(_WorkflowTaskBase):
+class WorkflowTaskUpdateV1(_WorkflowTaskBaseV1):
     """
     Class for `WorkflowTask` update.
     """
@@ -107,7 +107,7 @@ class WorkflowTaskUpdate(_WorkflowTaskBase):
         return m
 
 
-class _WorkflowBase(BaseModel):
+class _WorkflowBaseV1(BaseModel):
     """
     Base class for `Workflow`.
 
@@ -118,7 +118,7 @@ class _WorkflowBase(BaseModel):
     name: str
 
 
-class WorkflowRead(_WorkflowBase):
+class WorkflowReadV1(_WorkflowBaseV1):
     """
     Task for `Workflow` read from database.
 
@@ -131,8 +131,8 @@ class WorkflowRead(_WorkflowBase):
 
     id: int
     project_id: int
-    task_list: list[WorkflowTaskRead]
-    project: ProjectRead
+    task_list: list[WorkflowTaskReadV1]
+    project: ProjectReadV1
     timestamp_created: datetime
 
     _timestamp_created = validator("timestamp_created", allow_reuse=True)(
@@ -140,7 +140,7 @@ class WorkflowRead(_WorkflowBase):
     )
 
 
-class WorkflowCreate(_WorkflowBase):
+class WorkflowCreateV1(_WorkflowBaseV1):
     """
     Task for `Workflow` creation.
     """
@@ -149,7 +149,7 @@ class WorkflowCreate(_WorkflowBase):
     _name = validator("name", allow_reuse=True)(valstr("name"))
 
 
-class WorkflowUpdate(_WorkflowBase):
+class WorkflowUpdateV1(_WorkflowBaseV1):
     """
     Task for `Workflow` update.
 
@@ -173,7 +173,7 @@ class WorkflowUpdate(_WorkflowBase):
         return value
 
 
-class WorkflowImport(_WorkflowBase):
+class WorkflowImportV1(_WorkflowBaseV1):
     """
     Class for `Workflow` import.
 
@@ -181,13 +181,13 @@ class WorkflowImport(_WorkflowBase):
         task_list:
     """
 
-    task_list: list[WorkflowTaskImport]
+    task_list: list[WorkflowTaskImportV1]
 
     # Validators
     _name = validator("name", allow_reuse=True)(valstr("name"))
 
 
-class WorkflowExport(_WorkflowBase):
+class WorkflowExportV1(_WorkflowBaseV1):
     """
     Class for `Workflow` export.
 
@@ -195,10 +195,10 @@ class WorkflowExport(_WorkflowBase):
         task_list:
     """
 
-    task_list: list[WorkflowTaskExport]
+    task_list: list[WorkflowTaskExportV1]
 
 
-class WorkflowTaskStatusType(str, Enum):
+class WorkflowTaskStatusTypeV1(str, Enum):
     """
     Define the available values for the status of a `WorkflowTask`.
 

fractal_server/app/schemas/v2/__init__.py

@@ -0,0 +1,34 @@
+from .dataset import DatasetCreateV2  # noqa F401
+from .dataset import DatasetReadV2  # noqa F401
+from .dataset import DatasetUpdateV2  # noqa F401
+from .dumps import DatasetDumpV2  # noqa F401
+from .dumps import ProjectDumpV2  # noqa F401
+from .dumps import TaskDumpV2  # noqa F401
+from .dumps import WorkflowDumpV2  # noqa F401
+from .dumps import WorkflowTaskDumpV2  # noqa F401
+from .job import JobCreateV2  # noqa F401
+from .job import JobReadV2  # noqa F401
+from .job import JobStatusTypeV2  # noqa F401
+from .job import JobUpdateV2  # noqa F401
+from .manifest import ManifestV2  # noqa F401
+from .project import ProjectCreateV2  # noqa F401
+from .project import ProjectReadV2  # noqa F401
+from .project import ProjectUpdateV2  # noqa F401
+from .task import TaskCreateV2  # noqa F401
+from .task import TaskExportV2  # noqa F401
+from .task import TaskImportV2  # noqa F401
+from .task import TaskReadV2  # noqa F401
+from .task import TaskUpdateV2  # noqa F401
+from .task_collection import TaskCollectPipV2  # noqa F401
+from .task_collection import TaskCollectStatusV2  # noqa F401
+from .workflow import WorkflowCreateV2  # noqa F401
+from .workflow import WorkflowExportV2  # noqa F401
+from .workflow import WorkflowImportV2  # noqa F401
+from .workflow import WorkflowReadV2  # noqa F401
+from .workflow import WorkflowUpdateV2  # noqa F401
+from .workflowtask import WorkflowTaskCreateV2  # noqa F401
+from .workflowtask import WorkflowTaskExportV2  # noqa F401
+from .workflowtask import WorkflowTaskImportV2  # noqa F401
+from .workflowtask import WorkflowTaskReadV2  # noqa F401
+from .workflowtask import WorkflowTaskStatusTypeV2  # noqa F401
+from .workflowtask import WorkflowTaskUpdateV2  # noqa F401

fractal_server/app/schemas/v2/dataset.py

@@ -0,0 +1,89 @@
+from datetime import datetime
+from typing import Optional
+
+from pydantic import BaseModel
+from pydantic import Extra
+from pydantic import Field
+from pydantic import validator
+
+from .._validators import valstr
+from .._validators import valutc
+from ..v1.project import ProjectReadV1
+from .dumps import WorkflowTaskDumpV2
+from .workflowtask import WorkflowTaskStatusTypeV2
+from fractal_server.images import Filters
+
+
+class _DatasetHistoryItemV2(BaseModel):
+    """
+    Class for an item of `Dataset.history`.
+    """
+
+    workflowtask: WorkflowTaskDumpV2
+    status: WorkflowTaskStatusTypeV2
+    parallelization: Optional[dict]
+
+
+class DatasetStatusReadV2(BaseModel):
+    """
+    Response type for the
+    `/project/{project_id}/dataset/{dataset_id}/status/` endpoint
+    """
+
+    status: Optional[
+        dict[
+            str,
+            WorkflowTaskStatusTypeV2,
+        ]
+    ] = None
+
+
+# CRUD
+
+
+class DatasetCreateV2(BaseModel, extra=Extra.forbid):
+
+    name: str
+
+    read_only: bool = False
+    zarr_dir: str
+
+    filters: Filters = Field(default_factory=Filters)
+
+    # Validators
+    _name = validator("name", allow_reuse=True)(valstr("name"))
+
+
+class DatasetReadV2(BaseModel):
+
+    id: int
+    name: str
+
+    project_id: int
+    project: ProjectReadV1
+
+    history: list[_DatasetHistoryItemV2]
+    read_only: bool
+
+    timestamp_created: datetime
+
+    zarr_dir: str
+    filters: Filters = Field(default_factory=Filters)
+
+    # Validators
+    _timestamp_created = validator("timestamp_created", allow_reuse=True)(
+        valutc("timestamp_created")
+    )
+
+
+class DatasetUpdateV2(BaseModel):
+    class Config:
+        extra = "forbid"
+
+    name: Optional[str]
+    read_only: Optional[bool]
+    zarr_dir: Optional[str]
+    filters: Optional[Filters]
+
+    # Validators
+    _name = validator("name", allow_reuse=True)(valstr("name"))

fractal_server/app/schemas/v2/dumps.py

@@ -0,0 +1,87 @@
+"""
+
+Dump models differ from their Read counterpart in that:
+* They are directly JSON-able, without any additional encoder.
+* They may only include a subset of the Read attributes.
+
+These models are used in at least two situations:
+1. In the "*_dump" attributes of ApplyWorkflow models;
+2. In the `_DatasetHistoryItem.workflowtask` model, to trim its size.
+"""
+from typing import Optional
+
+from pydantic import BaseModel
+from pydantic import Extra
+from pydantic import root_validator
+
+from fractal_server.app.schemas.v1.dumps import TaskDumpV1
+from fractal_server.images import Filters
+
+
+class ProjectDumpV2(BaseModel, extra=Extra.forbid):
+
+    id: int
+    name: str
+    read_only: bool
+    timestamp_created: str
+
+
+class TaskDumpV2(BaseModel):
+    id: int
+    name: str
+    type: str
+
+    command_non_parallel: Optional[str]
+    command_parallel: Optional[str]
+    source: str
+    owner: Optional[str]
+    version: Optional[str]
+
+    input_types: dict[str, bool]
+    output_types: dict[str, bool]
+
+
+class WorkflowTaskDumpV2(BaseModel):
+    id: int
+    workflow_id: int
+    order: Optional[int]
+
+    input_filters: Filters
+
+    task_id: Optional[int]
+    task: Optional[TaskDumpV2]
+    task_legacy_id: Optional[int]
+    task_legacy: Optional[TaskDumpV1]
+
+    # Validators
+    @root_validator
+    def task_v1_or_v2(cls, values):
+        v1 = values.get("task_legacy_id")
+        v2 = values.get("task_id")
+        if ((v1 is not None) and (v2 is not None)) or (
+            (v1 is None) and (v2 is None)
+        ):
+            message = "both" if (v1 and v2) else "none"
+            raise ValueError(
+                "One and only one must be provided between "
+                f"'task_legacy_id' and 'task_id' (you provided {message})"
+            )
+        return values
+
+
+class WorkflowDumpV2(BaseModel):
+    id: int
+    name: str
+    project_id: int
+    timestamp_created: str
+
+
+class DatasetDumpV2(BaseModel):
+    id: int
+    name: str
+    project_id: int
+    read_only: bool
+    timestamp_created: str
+
+    zarr_dir: str
+    filters: Filters

fractal_server/app/schemas/v2/job.py

@@ -0,0 +1,114 @@
+from datetime import datetime
+from enum import Enum
+from typing import Optional
+
+from pydantic import BaseModel
+from pydantic import Extra
+from pydantic import validator
+from pydantic.types import StrictStr
+
+from .._validators import valstr
+from .._validators import valutc
+from .dumps import DatasetDumpV2
+from .dumps import ProjectDumpV2
+from .dumps import WorkflowDumpV2
+
+
+class JobStatusTypeV2(str, Enum):
+    """
+    Define the available job statuses
+
+    Attributes:
+        SUBMITTED:
+            The job was created. This does not guarantee that it was also
+            submitted to an executor (e.g. other errors could have prevented
+            this), nor that it is actually running (e.g. SLURM jobs could be
+            still in the queue).
+        DONE:
+            The job successfully reached its end.
+        FAILED:
+            The workflow terminated with an error.
+    """
+
+    SUBMITTED = "submitted"
+    DONE = "done"
+    FAILED = "failed"
+
+
+class JobCreateV2(BaseModel, extra=Extra.forbid):
+
+    first_task_index: Optional[int] = None
+    last_task_index: Optional[int] = None
+    slurm_account: Optional[StrictStr] = None
+    worker_init: Optional[str]
+
+    # Validators
+    _worker_init = validator("worker_init", allow_reuse=True)(
+        valstr("worker_init")
+    )
+
+    @validator("first_task_index", always=True)
+    def first_task_index_non_negative(cls, v, values):
+        """
+        Check that `first_task_index` is non-negative.
+        """
+        if v is not None and v < 0:
+            raise ValueError(
+                f"first_task_index cannot be negative (given: {v})"
+            )
+        return v
+
+    @validator("last_task_index", always=True)
+    def first_last_task_indices(cls, v, values):
+        """
+        Check that `last_task_index` is non-negative, and that it is not
+        smaller than `first_task_index`.
+        """
+        if v is not None and v < 0:
+            raise ValueError(
+                f"last_task_index cannot be negative (given: {v})"
+            )
+
+        first_task_index = values.get("first_task_index")
+        last_task_index = v
+        if first_task_index is not None and last_task_index is not None:
+            if first_task_index > last_task_index:
+                raise ValueError(
+                    f"{first_task_index=} cannot be larger than "
+                    f"{last_task_index=}"
+                )
+        return v
+
+
+class JobReadV2(BaseModel):
+
+    id: int
+    project_id: Optional[int]
+    project_dump: ProjectDumpV2
+    user_email: str
+    slurm_account: Optional[str]
+    workflow_id: Optional[int]
+    workflow_dump: WorkflowDumpV2
+    dataset_id: Optional[int]
+    dataset_dump: DatasetDumpV2
+    start_timestamp: datetime
+    end_timestamp: Optional[datetime]
+    status: str
+    log: Optional[str]
+    working_dir: Optional[str]
+    working_dir_user: Optional[str]
+    first_task_index: Optional[int]
+    last_task_index: Optional[int]
+    worker_init: Optional[str]
+
+    _start_timestamp = validator("start_timestamp", allow_reuse=True)(
+        valutc("start_timestamp")
+    )
+    _end_timestamp = validator("end_timestamp", allow_reuse=True)(
+        valutc("end_timestamp")
+    )
+
+
+class JobUpdateV2(BaseModel):
+
+    status: JobStatusTypeV2